Package org.biojava.nbio.structure.io.mmcif

Class SimpleMMcifParser

java.lang.Object
org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser
All Implemented Interfaces:
MMcifParser
public class SimpleMMcifParser extends Object implements MMcifParser
A simple mmCif file parser Usage: 
String file = "path/to/mmcif/file";
StructureIOFile pdbreader = new MMCIFFileReader();

Structure s = pdbreader.getStructure(file);
System.out.println(s);

// you can convert it to a PDB file...
System.out.println(s.toPDB());
For more documentation see http://biojava.org/wiki/BioJava:CookBook#Protein_Structure.
Since:
1.7
Author:
Andreas Prlic, Jose Duarte

  • Field Details

  • Constructor Details

    • SimpleMMcifParser

      public SimpleMMcifParser()

  • Method Details

    • addMMcifConsumer

      public void addMMcifConsumer(MMcifConsumer consumer)
      Description copied from interface: MMcifParser
      Add a MMcifConsumer that listens to even being triggered by the parser and processes the data into a backend provided by the Consumer.
      Specified by:
      addMMcifConsumer in interface MMcifParser
      Parameters:
      consumer - a consumer object.

    • clearConsumers

      public void clearConsumers()
      Description copied from interface: MMcifParser
      Remove all consumers from the parser.
      Specified by:
      clearConsumers in interface MMcifParser

    • removeMMcifConsumer

      public void removeMMcifConsumer(MMcifConsumer consumer)
      Description copied from interface: MMcifParser
      remove a single consumer from the parser
      Specified by:
      removeMMcifConsumer in interface MMcifParser

    • main

      public static void main(String[] args)

    • parse

      public void parse(InputStream inStream) throws IOException
      Description copied from interface: MMcifParser
      Start the actual parsing. The parser will trigger events that are defined by the MMcifConsumer class.
      Specified by:
      parse in interface MMcifParser
      Parameters:
      inStream - InputStream to parse from.
      Throws:
      IOException

    • parse

      public void parse(BufferedReader buf) throws IOException
      Description copied from interface: MMcifParser
      Start the actual parsing. The parser will trigger events that are defined by the MMcifConsumer class.
      Specified by:
      parse in interface MMcifParser
      Parameters:
      buf - a BufferedReader.
      Throws:
      IOException

    • triggerNewPdbxStructOper

      public void triggerNewPdbxStructOper(PdbxStructOperList structOper)

    • triggerNewStructNcsOper

      public void triggerNewStructNcsOper(StructNcsOper sNcsOper)

    • triggerNewAtomSites

      public void triggerNewAtomSites(AtomSites atomSites)

    • triggerGeneric

      public void triggerGeneric(String category, List<String> loopFields, List<String> lineData)

    • triggerNewEntity

      public void triggerNewEntity(Entity entity)

    • triggerNewEntityPolySeq

      public void triggerNewEntityPolySeq(EntityPolySeq epolseq)

    • triggerNewEntitySrcGen

      public void triggerNewEntitySrcGen(EntitySrcGen entitySrcGen)

    • triggerNewEntitySrcNat

      public void triggerNewEntitySrcNat(EntitySrcNat entitySrcNat)

    • triggerNewEntitySrcSyn

      public void triggerNewEntitySrcSyn(EntitySrcSyn entitySrcSyn)

    • triggerNewChemComp

      public void triggerNewChemComp(ChemComp cc)

    • triggerNewStructAsym

      public void triggerNewStructAsym(StructAsym sasym)

    • triggerNewPdbxEntityNonPoly

      public void triggerNewPdbxEntityNonPoly(PdbxEntityNonPoly pen)

    • triggerNewStructKeywords

      public void triggerNewStructKeywords(StructKeywords kw)

    • triggerNewRefine

      public void triggerNewRefine(Refine r)

    • triggerDocumentStart

      public void triggerDocumentStart()

    • triggerDocumentEnd

      public void triggerDocumentEnd()

    • triggerNewChemCompDescriptor

      public void triggerNewChemCompDescriptor(ChemCompDescriptor ccd)